tbuckley/cabot-search huggingface dataset:
Detection and subtyping of hepatic echinococcosis from plain CT images with deep learning: a retrospective, multicentre study
Authors: Zhan Wang, Haiyang Bian, Jiaqi Li, Jin Xu, Haining Fan, Xinze Wu, Yuntai Cao, Bin Guo, Xiaolei Xu, Haijiu Wang, Lingqiang Zhang, Hu Zhou, Jianfeng Fan, Youyou Ren, Yunping Geng, Xiaobin Feng, Luming Li, Lei Wei, Xuegong Zhang
Journal: The Lancet Digital Health (2023)

BackgroundHepatic echinococcosis is a severe endemic disease in some underdeveloped rural areas worldwide. Qualified physicians are in short supply in such areas, resulting in low rates of accurate diagnosis of this condition. In this study, we aimed to develop and evaluate an artificial intelligence (AI) system for automated detection and subtyping of hepatic echinococcosis using plain CT images with the goal of providing interpretable assistance to radiologists and clinicians.MethodsWe developed EDAM, an echinococcosis diagnostic AI system, to provide accurate and generalisable CT analysis for distinguishing hepatic echinococcosis from hepatic cysts and normal controls (no liver lesions), as well as subtyping hepatic echinococcosis as alveolar or cystic echinococcosis. EDAM includes a slice-level prediction model for lesion classification and segmentation and a patient-level diagnostic model for patient classification. We collected a plain CT database (n=700: 395 cystic echinococcosis, 122 alveolar echinococcosis, 130 hepatic cysts, and 53 normal controls) for developing EDAM, and two additional independent cohorts (n=156) for external validation of its performance and generalisation ability. We compared the performance of EDAM with 52 experienced radiologists in diagnosing and subtyping hepatic echinococcosis.FindingsEDAM showed reliable performance in patient-level diagnosis on both the internal testing data (overall area under the receiver operating characteristic curve [AUC]: 0·974 [95% CI 0·936–0·994]; accuracy: 0·952 [0·939–0·965] for cystic echinococcosis, 0·981 [0·973–0·989] for alveolar echinococcosis; sensitivity: 0·966 [0·951–0·979] for cystic echinococcosis, 0·944 [0·908–0·970] for alveolar echinococcosis) and the external testing set (overall AUC: 0·953 [95% CI 0·840–0·973]; accuracy: 0·929 [0·915–0·947] for cystic echinococcosis, 0·936 [0·919–0·950] for alveolar echinococcosis; sensitivity: 0·913 [0·879–0·944] for cystic echinococcosis, 0·868 [0·841–0·897] for alveolar echinococcosis). The sensitivity of EDAM was robust across images from different CT manufacturers. EDAM outperformed most of the enrolled radiologists in detecting both alveolar echinococcosis and cystic echinococcosis.InterpretationEDAM is a clinically applicable AI system that can provide patient-level diagnoses with interpretable results. The accuracy and generalisation ability of EDAM demonstrates its potential for clinical use, especially in underdeveloped areas.FundingProject of Qinghai Provincial Department of Science and Technology of China, National Natural Science Foundation of China, and Tsinghua-Fuzhou Institute of Data Technology Project.TranslationFor the Chinese translation of the abstract see Supplementary Materials section.
Tucatinib and Trastuzumab for Previously Treated Human Epidermal Growth Factor Receptor 2–Positive Metastatic Biliary Tract Cancer (SGNTUC-019): A Phase II Basket Study
Authors: Yoshiaki Nakamura, Nobumasa Mizuno, Yu Sunakawa, Jean-Luc Canon, Matthew D. Galsky, Erika Hamilton, Hidetoshi Hayashi, Guy Jerusalem, Seung Tae Kim, Keun-Wook Lee, Lionel Aurelien Kankeu Fonkoua, Bradley J. Monk, Danny Nguyen, Do-Youn Oh, Alicia Okines, David M. O'Malley, Paula Pohlmann, Martin Reck, Sang Joon Shin, Kazuki Sudo, Shunji Takahashi, Cedric Van Marcke, Evan Y. Yu, Roman Groisberg, Jorge Ramos, Sherry Tan, Thomas E. Stinchcombe, Tanios Bekaii-Saab
Journal: Journal of Clinical Oncology (2023)

To evaluate the efficacy and safety of tucatinib and trastuzumab in patients with previously treated human epidermal growth factor receptor 2-positive (HER2+) metastatic biliary tract cancer (mBTC).
Cystic Fibrosis Airways: Does Disease Stem from Faulty Stem Cells?
Authors: Katherine B. Hisert, Eszter K. Vladar
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Cystic Fibrosis Airways: Does Disease Stem from Faulty Stem Cells?." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Myelofibrosis: In Search for BETter Targeted Therapies
Authors: Giuseppe A. Palumbo, Andrea Duminuco
Journal: Journal of Clinical Oncology (2023)

Article Tools UNDERSTANDING THE PATHWAY Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES MANIFEST: Pelabresib in Combination With Ruxolitinib for Janus Kinase Inhibitor Treatment-Naïve Myelofibrosis. March 07, 2023 ARTICLE CITATION DOI: 10.1200/JCO.23.00833 Journal of Clinical Oncology - published online before print September 26, 2023 PMID: 37751563 Myelofibrosis: In Search for BETter Targeted Therapies Giuseppe A. Palumbo , MD, PhD1xGiuseppe A. PalumboSearch for articles by this author and Andrea Duminuco , MD2,3xAndrea DuminucoSearch for articles by this author Show More 1Department of Scienze Mediche, Chirurgiche e Tecnologie Avanzate “G.F. Ingrassia,” University of Catania, Catania, Italy2Postgraduate School of Hematology, University of Catania, Catania, Italy3Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom https://doi.org/10.1200/JCO.23.00833 First Page Full Text PDF Figures and Tables © 2023 by American Society of Clinical OncologyAUTHOR CONTRIBUTIONSConception and design: All authorsCollection and assembly of data: All authorsData analysis and interpretation: All authorsManuscript writing: All authorsFinal approval of manuscript: All authorsAccountable for all aspects of the work: All authorsAUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTERESTMyelofibrosis: In Search for BETter Targeted TherapiesThe following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated unless otherwise noted. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relationships may not relate to the subject matter of this manuscript. For more information about ASCO's conflict of interest policy, please refer to www.asco.org/rwc or ascopubs.org/jco/authors/author-center.Open Payments is a public database containing information reported by companies about payments made to US-licensed physicians (Open Payments).Giuseppe A. PalumboConsulting or Advisory Role: Novartis, AOP Orphan Pharmaceuticals, AbbVie, AstraZeneca, Celgene/Bristol Myers Squibb, GlaxoSmithKline, MorphosysSpeakers' Bureau: Novartis, Celgene/Bristol Myers Squibb, AbbVieTravel, Accommodations, Expenses: Takeda, Novartis, AbbVie, BeiGene, JanssenAndrea DuminucoHonoraria: EUSA Pharma, Celgene/Bristol Myers SquibbNo other potential conflicts of interest were reported. Companion MANIFEST: Pelabresib in Combination With Ruxolitinib for Janus Kinase Inhibitor Treatment-Naïve Myelofibrosis
Inner speech as language process and cognitive tool
Authors: Charles Fernyhough, Anna M. Borghi
Journal: Trends in Cognitive Sciences (2023)

Many people report a form of internal language known as inner speech (IS). This review examines recent growth of research interest in the phenomenon, which has broadly supported a theoretical model in which IS is a functional language process that can confer benefits for cognition in a range of domains. A key insight to have emerged in recent years is that IS is an embodied experience characterized by varied subjective qualities, which can be usefully modeled in artificial systems and whose neural signals have the potential to be decoded through advancing brain–computer interface technologies. Challenges for future research include understanding individual differences in IS and mapping form to function across IS subtypes.
Antidepressant and antipsychotic side-effects and personalised prescribing: a systematic review and digital tool development
Authors: Toby Pillinger, Oliver D Howes, Christoph U Correll, Stefan Leucht, Maximilian Huhn, Johannes Schneider-Thoma, Fiona Gaughran, Sameer Jauhar, Philip K McGuire, David M Taylor, Allan H Young, Robert A McCutcheon
Journal: The Lancet Psychiatry (2023)

Side-effects of psychiatric medication impair quality of life and functioning. Furthermore, they contribute to morbidity, mortality, stigma, and poor treatment concordance resulting in relapse of psychiatric illness. Guidelines recommend discussing side-effects with patients when making treatment decisions, but a synthesis of antidepressant and antipsychotic side-effects to guide this process is missing, and considering all side-effects is a complex, multidimensional process. We aimed to create comprehensive databases of antipsychotic and antidepressant side-effects, and a digital tool to support database navigation.
Quantitative estimates of preventable and treatable deaths from 36 cancers worldwide: a population-based study
Authors: Clara Frick, Harriet Rumgay, Jérôme Vignat, Ophira Ginsburg, Ellen Nolte, Freddie Bray, Isabelle Soerjomataram
Journal: The Lancet Global Health (2023)

BackgroundCancer is a leading cause of premature mortality globally. This study estimates premature deaths at ages 30–69 years and distinguishes these as deaths that are preventable (avertable through primary or secondary prevention) or treatable (avertable through curative treatment) in 185 countries worldwide.MethodsFor this population-based study, estimated cancer deaths by country, cancer, sex, and age groups were retrieved from the International Agency for Research on Cancer's GLOBOCAN 2020 database. Crude and age-adjusted cancer-specific years of life lost (YLLs) were calculated for 36 cancer types.FindingsOf the estimated all-ages cancer burden of 265·6 million YLLs, 182·8 million (68·8%) YLLs were due to premature deaths from cancer globally in 2020, with 124·3 million (68·0%) preventable and 58·5 million (32·0%) treatable. Countries with low, medium, or high human development index (HDI) levels all had greater proportions of YLLs at premature ages than very high HDI countries (68·9%, 77·0%, and 72·2% vs 57·7%, respectively). Lung cancer was the leading contributor to preventable premature YLLs in medium to very high HDI countries (17·4% of all cancers, or 29·7 million of 171·3 million YLLs), whereas cervical cancer led in low HDI countries (26·3% of all preventable cancers, or 1·83 million of 6·93 million YLLs). Colorectal and breast cancers were major treatable cancers across all four tiers of HDI (25·5% of all treatable cancers in combination, or 14·9 million of 58·5 million YLLs).InterpretationAlongside tailored programmes of early diagnosis and screening linked to timely and comprehensive treatment, greater investments in risk factor reduction and vaccination are needed to address premature cancer inequalities.FundingErasmus Mundus Exchange Programme and the International Agency for Research on Cancer.TranslationsFor the German, French, Spanish and Chinese translations of the abstract see Supplementary Materials section.
MELD 3.0 in Advanced Chronic Liver Disease
Authors: Nikhilesh R. Mazumder, Robert J. Fontana
Journal: Annual Review of Medicine (2023)

The MELD (model for end-stage liver disease) 3.0 score was developed to replace the MELD-Na score that is currently used to prioritize liver allocation for cirrhotic patients awaiting liver transplantation in the United States. The MELD 3.0 calculator includes new inputs from patient sex and serum albumin levels and has new weights for serum sodium, bilirubin, international normalized ratio, and creatinine levels. It is expected that use of MELD 3.0 scores will reduce overall waitlist mortality modestly and improve access for female liver transplant candidates. The utility of MELD 3.0 and PELD cre (pediatric end-stage liver disease, creatinine) scores for risk stratification in cirrhotic patients undergoing major abdominal surgery, placement of a transjugular intrahepatic portosystemic shunt, and other interventions requires further study. This article reviews the background of the MELD score and the rationale to create MELD 3.0 as well as potential implications of using this newer risk stratification tool in clinical practice.
Exposure to Perfluoroalkyl Substances and Associations with Pubertal Onset and Serum Reproductive Hormones in a Longitudinal Study of Young Girls in Greater Cincinnati and the San Francisco Bay Area
Authors: Susan M. Pinney, Cecily S. Fassler, Gayle C. Windham, Robert L. Herrick, Changchun Xie, Lawrence H. Kushi, Frank M. Biro
Journal: Environmental Health Perspectives (2023)

Background: Per- and polyfluoroalkyl substances (PFAS), endocrine disrupting chemicals with worldwide exposure, cause changes in mammary gland development in rodents. A few human studies report delay in pubertal events with increasing perfluorooctanoic acid (PFOA) exposure, but to our knowledge none have examined reproductive hormone levels at thelarche. Methods: In a cohort of Greater Cincinnati (GC) and San Francisco Bay Area (SFBA) girls recruited at 6–8 years of age, clinical examinations were conducted annually or semiannually with sequential Tanner staging. PFAS concentrations were measured in the first serum sample of 704 girls. In 304 GC girls, estradiol (E2), estrone (E1), testosterone (T), and dihydroepiandrosterone sulfate (DHEAS) were measured in serum at four time points around puberty. Relationships between PFAS and age at thelarche, pubarche, and menarche were analyzed using survival and structural equation models. The association between PFAS and reproductive hormones was assessed using linear regression models. Results: Median PFOA serum concentrations in GC (N=353, 7.3 ng/mL) and the SFBA (N=351, 5.8 ng/mL) were higher than in the U.S. population. In multivariable Cox proportional hazard models [adjusted for race, body mass index (BMI)], increasing serum log-transformed PFOA was associated with a delay in pubarche [hazard ratio (HR)=0.83; 95% CI: 0.70, 0.99] and menarche (HR=0.04; 95% CI: 0.01, 0.25). Structural equation models indicated a triangular relationship between PFOA, BMI percentile, and the age at the pubertal milestone. Increased PFOA had a statistically significant direct effect of delay on all three milestones, as did BMI. Perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDeA), and 2-(N-methyl-perfluorooctane sulfonamido) acetic acid (Me-PFOSA-AcOH) also were associated with later thelarche, and Me-PFOSA-AcOH also with later pubarche. PFOA was inversely associated with DHEAS (p<0.01), E1 (p=0.04), and T (p=0.03) concentrations at 6 months prior to puberty. Conclusions: PFAS may delay pubertal onset through the intervening effects on BMI and reproductive hormones. The decreases in DHEAS and E1 associated with PFOA represent biological biomarkers of effect consistent with the delay in onset of puberty. https://doi.org/10.1289/EHP11811
Evaluating socioeconomic inequalities in influenza vaccine uptake during the COVID-19 pandemic: A cohort study in Greater Manchester, England
Authors: Ruth Elizabeth Watkinson, Richard Williams, Stephanie Gillibrand, Luke Munford, Matt Sutton
Journal: PLoS Medicine (2023)

There are known socioeconomic inequalities in annual seasonal influenza (flu) vaccine uptake. The Coronavirus Disease 2019 (COVID-19) pandemic was associated with multiple factors that may have affected flu vaccine uptake, including widespread disruption to healthcare services, changes to flu vaccination eligibility and delivery, and increased public awareness and debate about vaccination due to high-profile COVID-19 vaccination campaigns. However, to the best of our knowledge, no existing studies have investigated the consequences for inequalities in flu vaccine uptake, so we aimed to investigate whether socioeconomic inequalities in flu vaccine uptake have widened since the onset of the COVID-19 pandemic.
Precancerous nature of intestinal metaplasia with increased chance of conversion and accelerated DNA methylation
Authors: Chihiro Takeuchi, Satoshi Yamashita, Yu-Yu Liu, Hideyuki Takeshima, Akiko Sasaki, Masahide Fukuda, Taiki Hashimoto, Tomoaki Naka, Kenichi Ishizu, Shigeki Sekine, Takaki Yoshikawa, Akinobu Hamada, Nobutake Yamamichi, Mitsuhiro Fujishiro, Toshikazu Ushijima
Journal: Gut (2023)

The presence of intestinal metaplasia (IM) is a risk factor for gastric cancer. However, it is still controversial whether IM itself is precancerous or paracancerous. Here, we aimed to explore the precancerous nature of IM by analysing epigenetic alterations.
Exploring the dynamics of Borrelia burgdorferi sensu lato antibodies—a registry-based study on laboratory data from Sweden and Denmark
Authors: Marc Westerholt, Karen Angeliki Krogfelt, Ram Benny Dessau, Lukas Frans Ocias
Journal: Clinical Microbiology and Infection (2023)

Lyme borreliosis (LB) is the most common tick-transmitted infection in the northern hemisphere and is caused by bacteria in the Borrelia burgdorferi sensu lato (Bbsl)-complex. The diagnosis is partially based on serology, and clinicians often take follow-up serum samples to look for seroconversion or an increase in IgG-antibody levels. In this registry-based study, we proposed a method for determining actual changes in IgG and examined antibody reactivity and decay.Serological data from the departments of clinical microbiology at Karlstad Hospital, Sweden, and Slagelse Hospital, Denmark, were used to calculate a seroreactivity cut-off (SCOFF), above which changes between two samples from the patient cannot be explained by random variation. Increases in IgG reactivity as well as IgG and IgM decay were illustrated using time-to-event analysis and the SCOFF.A total of 44,861 serum samples from 34,157 patients were tested for Bbsl-antibodies. Of the 4301 patients with follow-up samples taken within 100 days, 201 (4.67%) were above the SCOFF of 1.42 with a median time to follow-up sample of 36 days (interquartile range: 21). IgG demonstrated longer median time for all antibody levels (indeterminate: 4.6 years, low: 7.0 years, moderate-high: 8.8 years) than IgM antibodies (indeterminate: 2.1 years, low: 3.9 years, moderate-high: 6.8 years) and higher initial antibody levels persisted significantly longer for both IgG and IgM antibodies (p < 0.001). Of the 7868 patients with follow-up samples, isolated IgM reactivity preceded an increase in IgG reactivity in 18 patients (0.23%).The SCOFF indicated little biological and random variation for Bbsl-specific IgG antibodies on the platforms used during the study. In most follow-up samples, both IgG and IgM antibodies persisted for years, with longer seropositivity associated with high initial antibody levels and IgG-type antibodies. The diagnostic value of isolated IgM reactivity was limited.
Kinetics and durability of nucleocapsid-specific antibodies after SARS-CoV-2 reinfection
Authors: Shohei Yamamoto, Tetsuya Mizoue, Maki Konishi, Yusuke Oshiro, Natsumi Inamura, Takashi Nemoto, Tomofumi Tan, Wataru Sugiura, Norio Ohmagari
Journal: Journal of Infection (2023)
Efficacy and safety of anti-COVID-19 vaccination in patients with autoimmune blistering diseases: A French national study
Authors: Sokounthie Ou, Emmanuelle Tancrède-Bohin, Marina Alexandre, Saskia Ingen-Housz-Oro, Marion Castel, Sébastien Debarbieux, Sophie Duvert-Lehembre, Maria Polina Konstantinou, Claire Abasq, Clémence Berthin, Caroline Couzan, Clémence Lepelletier, Lamia Jelti, Julie Bouteiller, Andreea Calugareanu, Marie Véron, Frédéric Caux, Pascal Joly, Bérenger Thomas, Manuelle Viguier
Journal: Journal of the American Academy of Dermatology (2023)
What should I do if I am sexually assaulted at work?
Authors: Abi Rimmer
Journal: BMJ (2023)

Put yourself firstBecky Cox, co-founder of Surviving in Scrubs, says, "There is no right or wrong way to feel after being sexually assaulted.It's normal to feel a range of emotions from anxiety to anger-even numbness.Working as doctors we anticipate the stress of long hours and high workloads, but
del(8p) and TNFRSF10B loss are associated with a poor prognosis and resistance to fludarabine in chronic lymphocytic leukemia
Authors: Ludovic Jondreville, Lea Dehgane, Cecile Doualle, Luce Smagghe, Beatrice Grange, Frederic Davi, Leticia K. Lerner, Delphine Garnier, Clotilde Bravetti, Olivier Tournilhac, Damien Roos-Weil, Marouane Boubaya, Elise Chapiro, Santos A. Susin, Florence Nguyen-Khac
Journal: Leukemia (2023)
Author Correction: Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk
Authors: Naomi Wilcox, Martine Dumont, Anna González-Neira, Sara Carvalho, Charles Joly Beauparlant, Marco Crotti, Craig Luccarini, Penny Soucy, Stéphane Dubois, Rocio Nuñez-Torres, Guillermo Pita, Eugene J. Gardner, Joe Dennis, M. Rosario Alonso, Nuria Álvarez, Caroline Baynes, Annie Claude Collin-Deschesnes, Sylvie Desjardins, Heiko Becher, Sabine Behrens, Manjeet K. Bolla, Jose E. Castelao, Jenny Chang-Claude, Sten Cornelissen, Thilo Dörk, Christoph Engel, Manuela Gago-Dominguez, Pascal Guénel, Andreas Hadjisavvas, Eric Hahnen, Mikael Hartman, Belén Herráez, Benita Kiat-Tee Tan, Veronique Kiak Mien Tan, Su-Ming Tan, Geok Hoon Lim, Ern Yu Tan, Peh Joo Ho, Alexis Jiaying Khng, Audrey Jung, Renske Keeman, Marion Kiechle, Jingmei Li, Maria A. Loizidou, Michael Lush, Kyriaki Michailidou, Mihalis I. Panayiotidis, Xueling Sim, Soo Hwang Teo, Jonathan P. Tyrer, Lizet E. van der Kolk, Cecilia Wahlström, Qin Wang, John R. B. Perry, Javier Benitez, Marjanka K. Schmidt, Rita K. Schmutzler, Paul D. P. Pharoah, Arnaud Droit, Alison M. Dunning, Anders Kvist, Peter Devilee, Douglas F. Easton, Jacques Simard
Journal: Nature Genetics (2023)
The experience of navigating sexuality for transgender and gender non-conforming people: a meta-ethnographic review
Authors: Alastair Pipkin, Luke Ward, Sue Cotton, Christina Shearn
Journal: International Journal of Transgender Health (2023)

The current research builds on a previous review of the literature which explored sexuality during gender transition. There has been increased attention toward TGNC people across academic, political, and healthcare fields since the previous review, as well as shifts in language use and health interventions, justifying a need for more contemporary understandings.
The immunome of mobilized peripheral blood stem cells is predictive of long-term outcomes and therapy-related myeloid neoplasms in patients with multiple myeloma undergoing autologous stem cell transplant
Authors: Saurabh Zanwar, Eapen K. Jacob, Carl Greiner, Kevin Pavelko, Michael Strausbauch, Emilie Anderson, Arini Arsana, Megan Weivoda, Mithun Vinod Shah, Taxiarchis Kourelis
Journal: Blood Cancer Journal (2023)

Abstract Upfront autologous stem cell transplant (ASCT) is the standard of care for newly diagnosed multiple myeloma (MM) patients. However, relapse is ubiquitous and therapy-related myeloid neoplasms (t-MN) post-ASCT are commonly associated with poor outcomes. We hypothesized that the enrichment of abnormal myeloid progenitors and immune effector cells (IEC) in the peripheral blood stem cells (PBSCs) is associated with a higher risk of relapse and/or development of t-MN. We performed a comprehensive myeloid and lymphoid immunophenotyping on PBSCs from 54 patients with MM who underwent ASCT. Median progression-free (PFS), myeloid neoplasm-free (MNFS), and overall survival (OS) from ASCT were 49.6 months (95% CI: 39.5-Not Reached), 59.7 months (95% CI: 55–74), and 75.6 months (95% CI: 62–105), respectively. Abnormal expression of CD7 and HLA-DR on the myeloid progenitor cells was associated with an inferior PFS, MNFS, and OS. Similarly, enrichment of terminally differentiated (CD27/CD28 - , CD57/KLRG1 + ) and exhausted (TIGIT/PD-1 + ) T-cells, and inhibitory NK-T like (CD159a + /CD56 + ) T-cells was associated with inferior PFS, MNFS, and OS post-transplant. Our observation of abnormal myeloid and IEC phenotype being present even before ASCT and maintenance therapy suggests an early predisposition to t-MN and inferior outcomes for MM, and has the potential to guide sequencing of future treatment modalities.